magenpy is a Python package for modeling and analyzing statistical genetics data.
The package provides tools for:
- Reading and processing genotype data in
plinkBED format. - Efficient LD matrix construction and storage in Zarr array format.
- Data structures for harmonizing various GWAS data sources.
- Includes parsers for commonly used GWAS summary statistics formats.
- Simulating polygenic traits (continuous and binary) using complex genetic architectures.
- Multi-cohort simulation scenarios (beta)
- Simulations incorporating functional annotations in the genetic architecture (beta)
- Interfaces for performing association testing on simulated and real phenotypes.
- Preliminary support for processing and integrating genomic annotations with other data sources.